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<title>MarvinView Example - XYZ animations</title>
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<h1>MarvinView Example - XYZ animations</h1>

In this example a molecular dynamic simulation is shown about the thermal motion of a segment of
a protein alpha helix. The simulation is provided by Raul E. Cachau &lt;cachau@ncifcrf.gov&gt;.

<p><center>
<script LANGUAGE="JavaScript1.1" SRC="../../../marvin.js"></script>
<script LANGUAGE="JavaScript1.1">
<!--
mview_begin("../../..", 561, 300);
mview_param("molbg", "#000000");
mview_param("atomSymbolsVisible", "false");
mview_param("animSync", "true");
mview_param("spin1", "30,1,-1,0");
mview_param("navmode", "rot3d");
mview_param("rendering", "spacefill");
mview_param("rows", "1");
mview_param("cols", "2");
mview_param("border", "1");
mview_param("layout", ":2:1:M:1:0:1:1:L:0:0:1:1:c:n:1:1");
mview_param("param", ":M:280:280:L:10b");
mview_param("cell0", ":../../../mols-3d/all_atoms_cyclic_traj.xyz.gz:All atoms");
mview_param("cell1", ":../../../mols-3d/backbone_atoms_cyclic_traj.xyz.gz:Backbone atoms only");
mview_end();
//-->
</script>
</center>

The <a HREF="../../../help/developer/viewman.html#3d.animSync">animSync</a> parameter is used to
synchronize the animation in the two cells.
The <a HREF="../../../help/developer/viewman.html#3d.spin">spin1</a> parameter sets the spinning rate
and axis for the right cell.

<blockquote>
<pre>
<strong>&lt;script LANGUAGE</strong>=&quot;JavaScript1.1&quot; <strong>SRC</strong>=&quot;../../../<a HREF="../marvin.js.txt">marvin.js</a>&quot;<strong>&gt;</strong><strong>&lt;/script&gt;</strong>
<strong>&lt;script LANGUAGE</strong>=&quot;JavaScript1.1&quot;<strong>&gt;</strong>
<strong>&lt;!--</strong>
<strong>mview_begin(</strong>&quot;../../..&quot;<strong>,</strong> 561<strong>,</strong> 300<strong>);</strong>
<strong>mview_param(</strong>&quot;<a HREF="../../../help/developer/viewman.html#parameters.molbg">molbg</a>&quot;<strong>,</strong> &quot;#000000&quot;<strong>);</strong>
<strong>mview_param(</strong>&quot;<a HREF="../../../help/developer/viewman.html#parameters.atomSymbolsVisible">atomSymbolsVisible</a>&quot;<strong>,</strong> &quot;false&quot;<strong>);</strong>
<strong>mview_param(</strong>&quot;<a HREF="../../../help/developer/viewman.html#3d.animSync">animSync</a>&quot;<strong>,</strong> &quot;true&quot;<strong>);</strong>
<strong>mview_param(</strong>&quot;<a HREF="../../../help/developer/viewman.html#3d.spin">spin1</a>&quot;<strong>,</strong> &quot;30,1,-1,0&quot;<strong>);</strong>
<strong>mview_param(</strong>&quot;<a HREF="../../../help/developer/viewman.html#parameters.navmode">navmode</a>&quot;<strong>,</strong> &quot;rot3d&quot;<strong>);</strong>
<strong>mview_param(</strong>&quot;<a HREF="../../../help/developer/viewman.html#3d.rendering">rendering</a>&quot;<strong>,</strong> &quot;spacefill&quot;<strong>);</strong>
<strong>mview_param(</strong>&quot;<a HREF="../../../help/developer/viewman.html#advanced.rows">rows</a>&quot;<strong>,</strong> &quot;1&quot;<strong>);</strong>
<strong>mview_param(</strong>&quot;<a HREF="../../../help/developer/viewman.html#advanced.cols">cols</a>&quot;<strong>,</strong> &quot;2&quot;<strong>);</strong>
<strong>mview_param(</strong>&quot;<a HREF="../../../help/developer/viewman.html#advanced.border">border</a>&quot;<strong>,</strong> &quot;1&quot;<strong>);</strong>
<strong>mview_param(</strong>&quot;<a HREF="../../../help/developer/viewman.html#advanced.layout">layout</a>&quot;<strong>,</strong> &quot;:2:1:M:1:0:1:1:L:0:0:1:1:c:n:1:1&quot;<strong>);</strong>
<strong>mview_param(</strong>&quot;<a HREF="../../../help/developer/viewman.html#advanced.param">param</a>&quot;<strong>,</strong> &quot;:M:280:280:L:10b&quot;<strong>);</strong>
<strong>mview_param(</strong>&quot;<a HREF="../../../help/developer/viewman.html#advanced.cell">cell0</a>&quot;<strong>,</strong> &quot;:../../../mols-3d/all_atoms_cyclic_traj.xyz.gz:All atoms&quot;<strong>);</strong>
<strong>mview_param(</strong>&quot;cell1&quot;<strong>,</strong> &quot;:../../../mols-3d/backbone_atoms_cyclic_traj.xyz.gz:Backbone atoms only&quot;<strong>);</strong>
<strong>mview_end();</strong>
<strong>//--&gt;</strong>
<strong>&lt;/script&gt;</strong>
</pre>
</blockquote>

<p>Note, that this animation does not work in Netscape versions earlier than 4.0
because Java 1.1 is needed for unpacking the gzipped files.</p>

<p>
<center><div class="lenia">&nbsp;</div></center>
<p>

The next example shows how to
<a HREF="stereoconfig.html">visualize chirality</a> in the viewer.

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